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Figure S1: Clustering analysis of the expression ratio of the sense and antisense pair of transcripts
Flag
dT Random
A
A
C
D
E
B
F
(Protein-Coding / Non-Coding)
C
(Non-Coding / Non-Coding)
B
Normal Cancer
D
Sense : Antisense = 3:1
Sense : Antisense = 1:1
E
F
(Protein-Coding / Protein-Coding)
Sense : Antisense = 1:3
Figure S2: Changes in expression for sense-antisense gene pairs in cancer tissues, compared with
surrounding normal tissues.
(a) Plots of (protein-coding, protein-coding) pairs
1.5
Antisense Change (log10 scale)
1
0.5
0
-1.5
-1
-0.5
0
-0.5
-1
-1.5
Sense Change (log10 scale)
0.5
1
1.5
All other data
Sense up, Antis down
Sense down, Antis up
Figure S2: Changes in expression for sense-antisense gene pairs in cancer tissues, compared with
surrounding normal tissues.
(b) Plots of (protein-coding, non-coding) pairs
1.5
Antisense Change (log10 scale)
1
0.5
0
-1.5
-1
-0.5
0
-0.5
-1
-1.5
Sense Change (log10 scale)
0.5
1
1.5
All other data
Sense up, Antis down
Sense down, Antis up
Figure S2: Changes in expression for sense-antisense gene pairs in cancer tissues, compared with
surrounding normal tissues.
(c) Plots of (non-coding, non-coding) pairs
1.5
Antisense Change (log10 scale)
1
0.5
0
-1.5
-1
-0.5
0
-0.5
-1
-1.5
Sense Change (log10 scale)
0.5
1
1.5
All other data
Sense up, Antis down
Sense down, Antis up
Figure S3: Changes in expression for sense-AFAS gene pairs in cancer tissues, compared with surrounding
normal tissues.
1.5
1
AFAS change (log scale)
0.5
0
-1.5
-1
-0.5
0
-0.5
-1
-1.5
Sense change (log scale)
0.5
1
1.5
All other data
Sense up, AFAS down
Sense down, AFAS up
Figure S4: Clustering analysis of
the expression ratio of wellknown genes (sense transcripts)
and their putative antisense
transcripts.
Flag
dT Random
A
A
C
D
E
B
C
D
B
Sense : AFAS = 3:1
Sense : AFAS = 1:1
E
Normal Cancer
Sense : AFAS = 1:3
Figure S5: Expression intensities detected by probes designed for the sense gene U69611 and its
corresponding AFAS transcript.
Expressional intensity of sense gene
500
NC
400
300
200
100
9613299
9547332
Truncated
Truncated
100
200
300
NC
400
500
Expressional intensity of AFAS gene
Figure S6: Average Expression levels detected by AFAS probes within every 500 bases with respect to the
both termini of sense transcripts.
4000
Average Intensity
3500
Normal
Cancer
3000
2500
2000
1500
1000
500
0
-1
-2
-3
-4
-5
5
4
3
2
1
Probe Position
500 bp
500 bp
-1
-2
Sense transcript
500 bp
500 bp
2
1